FLaG (Frequency‑Domain Latent‑attention Gated Pooling) is a plug‑in token‑aggregation module that transforms encoder outputs into the Fourier domain, summarizes spectral tokens with learnable latent queries, applies a sample‑conditioned channel gate, and reconstructs modulated token representations for downstream pooling. The method is evaluated on antimicrobial peptide activity prediction, CIFAR‑10/100 image classification, and several RoBERTa language tasks, achieving state‑of‑the‑art performance on most metrics. Analyses show that FLaG emphasizes low‑frequency components while selectively amplifying high‑frequency signals in later layers, providing a transferable frequency‑domain bias across protein, visual, and textual representations.
arXiv:2606. 08191v1 Announce Type: cross Abstract: Token aggregation is a common bottleneck in models that map token representations to sample-level predictions, yet most pooling methods operate only in the original token domain.
The study demonstrates that a simple, sequence-only approach using 330 interpretable descriptors and the TabPFN tabular foundation model can outperform complex multimodal deep learning methods for multi-label antimicrobial peptide activity prediction. On the ESCAPE benchmark (82,359 peptides, five labels), a label‑powerset TabPFN model achieved a mean average precision of 77.8%, surpassing the previous best of 72.1%. The approach also shows that predicted structure is unnecessary, that a small set of global physicochemical scalars can recover most performance, and that modeling label dependence benefits rare activities and informs assay prioritization.
GyroNovo is a new framework for de novo peptide sequencing that improves fragment imputation by guiding the process with decoder errors observed during training. It introduces mass-aware attention using rotary embeddings to encode pairwise mass differences between spectral peaks, and creates easy and hard augmented views of spectra to train the decoder under varying corruption levels. Experiments on NovoBench demonstrate significant gains, with about 9 percentage points higher peptide-level precision and 7 percentage points higher amino-acid-level precision compared to the state-of-the-art baseline.
Freeze, Diffuse, Decode (FDD) is a diffusion-based framework that adapts pre‑trained transformer embeddings to downstream tasks while preserving their geometric structure. By propagating supervised signals along the intrinsic manifold of frozen embeddings, FDD produces low‑dimensional, predictive, and interpretable representations. In antimicrobial peptide design, these representations support property prediction, retrieval, and latent‑space interpolation.
Antimicrobial peptides (AMPs) often act against multiple pathogen classes, making multi-label activity prediction a more realistic screening target than binary antimicrobial classification. The ESCAPE...
arXiv:2607. 15047v1 Announce Type: cross Abstract: Mild Cognitive Impairment is a critical early stage of cognitive decline that frequently precedes Alzheimer's disease, yet its automated detection from neuropsychological drawing tests remains fundamentally constrained by data scarcity, class imbalance, and diagnostic ambiguity near clinical boundaries.
The study evaluates 4‑bit quantization and low‑rank adapter fine‑tuning (QLoRA) on several large protein language models, finding that many model‑task pairs retain over 90% of full fine‑tuning performance while achieving up to 90% GPU memory savings. QLoRA preserves early‑layer representations and induces task‑specific changes in later layers, closely resembling full fine‑tuning with smaller representational shifts. For generative models, 4‑bit quantization largely maintains structural and sequence‑level properties, though token‑level analysis reveals model‑dependent changes in autoregressive output distributions.
arXiv:2511.23120v2 Announce Type: replace Abstract: Pretrained transformers provide rich, general-purpose embeddings, which are transferred to downstream tasks. However, current transfer strategies:...
arXiv:2608.30975v1 Announce Type: cross Abstract: Cardiac magnetic resonance imaging (CMR) produces rich sequential data such as temporal cine videos and spatial LGE/mapping stacks, yet most deep lea...
arXiv:2607. 14070v1 Announce Type: cross Abstract: Genomic foundation models such as Evo 2 learn rich sequence representations, but their value for biosecurity screening is largely unexplored.
arXiv:2602. 22822v3 Announce Type: replace Abstract: Tandem mass spectrometry (MS/MS) is central to small molecule identification, but current deep learning systems for spectrum prediction still remain difficult to evaluate and deploy in practice.
arXiv:2606. 18703v1 Announce Type: new Abstract: Pretrained biological language models expose per-token probability distributions through masked-token prediction, providing the likelihood interface central to sequence design, variant scoring, and mechanistic interpretation.